5XB3

ADP-dTMP bound Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PBR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7	295	0.2M Ammonium citrate tribasic, 20% w/v Polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.54	α = 90.97
b = 52.98	β = 90.69
c = 53.78	γ = 109.6

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2014-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.9537	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.77	53.76	92	0.073	0.999	15.4	5		39574			19.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.77	1.87	84.6		0.604	0.816		4.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2PBR	1.77	53.76	37728	1844	91.97	0.16485	0.16252	0.21263	RANDOM	20.547

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.79	-0.25	1.13	0.41	1.59	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.841
r_dihedral_angle_4_deg	17.935
r_dihedral_angle_3_deg	14.319
r_dihedral_angle_1_deg	5.991
r_long_range_B_refined	5.092
r_long_range_B_other	5.026
r_scangle_other	4.242
r_scbond_it	2.842
r_scbond_other	2.826
r_mcangle_it	2.423
r_mcangle_other	2.423
r_angle_refined_deg	2.082
r_mcbond_it	1.749
r_mcbond_other	1.74
r_angle_other_deg	1.072
r_chiral_restr	0.121
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3080
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms	96

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing